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BIOL 2020 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

What is the point of no return in the cell cycle?

(if the cell cycle does not finish after this the cell dies)

A

Transition from G1 to S phase

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2
Q

What does Kinase do?

A

Uses ATP to phosphorolate Proteins

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3
Q

What is Kinase?

A

An enzyme

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4
Q

What are Phosphotases

A

A family of Enzymes

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5
Q

What do phosphotases do?

A

They remove phosphate groups from proteins

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6
Q

What activates Kinases?

(CDKs)

A

Cyclin

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7
Q

What are the two roles of Cyclin?

A

Activate Kinases and give Kinases greater specificity.

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8
Q

When is S-Cyclin and M-Cyclin synthesized?

A

At the very beginning of S and M phase respectively.

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9
Q

What does the production of S-Cyclin and M-Cyclin do?

A

Tells the cell to beggin S and M phase respectively.

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10
Q

What does P27 do to activated CDKs?

A

It deactivates them

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11
Q

What does the S in S phase stand for?

A

DNA Synthesis

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12
Q

Where does DNA replication start along a chromosome?

A

Replication Origin Sites

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13
Q

What happens at replication forks?

A

Parent DNA is unzipped and new DNA is synthesized

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14
Q

How many DNA polymerases per replication fork?

A

Two

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15
Q

Which direction does DNA polymerase run on the template strand?

A

3’ to 5’

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16
Q

What direction is new DNA synthesized?

A

5’ to 3’

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17
Q

What does DNA polymerase need to start making new DNA?

A

A 3’ OH group called a primer

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18
Q

What does primase do?

A

Provides primers for DNA polymerase to start replicating

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19
Q

What does topoisomerase do in DNA replication?

A

Cuts one strand of DNA infront of replication fork to relieve tension

(Ligase fixes the cut)

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20
Q

Approximately how long are okazaki fragments?

A

200 bp

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20
Q

What are telomeres?

A

Sequences marking the ends of DNA
In vertebrates - 2500* TTAGGG

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21
Q

What does Telomerase do?

A

Adds new telomere sequences to the ends of DNA

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21
Q

What are the stages of M phase?

A

Propase, prometaphase, metaphase, anaphase, and telophase

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22
Q

Is signal induced endocytosis or constitutive endocytosis more common?

A

Signal induced

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23
Q

Low-density lipoproteins do what?

A

They transport fat through the blood stream

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24
Q

What makes Low-density lipoproteins unique?

A

They have a mono layer lipid membrane

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25
Q

How are endosomes similar to the golgi?

A

They play a role in sorting cell materials

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26
Q

What do lysosomes do?

A

They degrade unwanted cell materials into the component parts

(monomers)

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27
Q

How much energy is required for protein degredation?

A

none, degredation is energetically favorable

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28
Q

What does Ubiquitin do?

A

Marks proteins for degredation by binding to them

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29
Q

How does Ubiquitin bind to proteins?

A

The Ubiquitin C terminus binds covalently to the amino acid side chains of proteins

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30
Q

What are the names of the enzymes involved in the ubiquitin system?

A

E1, E2, and E3

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31
Q

Degredation is done in what protein?

A

Proteasomes

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32
Q

Where are proteasomes found in the cell?

A

Cytoplasm and Nucleus

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33
Q

What does ESCRT stand for?

A

Endosomal Sorting Complex Required of Transport

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34
Q

Where are ESCRT proteins found?

A

The cytoplasmic side of vesicle membranes

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35
Q

What does autophogy do?

A

delivers large intracelular material to lysosomes for degredation

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36
Q

What are the phases of the cell cycle?

A

G1, S, G2, M, and division

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37
Q

What do snares do for vesicles?

A

They pull vesicles to a mebrane through the H2O barrier.

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38
Q

What does the RAB protein do?

A

It tells the cell where it came form

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39
Q

What typically needs to happen before new proteins can leave the ER?

A

The protein needs to finish folding

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40
Q

What does glycosylation indicate?

A

Proteins were synthesized in the ER

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41
Q

What cleaves the N terminus sequence as proteins are built in the ER Lumen?

A

Signal Peptidase

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42
Q

What are the black dots on the ER?

A

Ribosomes

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43
Q

What are the three binding sites of ribosomes?

A

E-site, P-site, and A-site

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44
Q

Where does transcription happen?

A

nucleus

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45
Q

Where does translation happen?

A

Cytoplasm

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46
Q

What prtoects the 3’ end of mRNA

A

the poly A tail

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47
Q

What are exons?

A

the coding regions of the gene

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48
Q

What does intron splicing do?

A

signals to export mRNA

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49
Q

Are exons or introns removed to form mature mRNA?

A

introns

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50
Q

What is the first thing that happens to new RNA?

A

It gets a 5’ cap

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51
Q

What does the 5’ cap do for RNA?

A

It helps protect (stabilize) the RNA

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52
Q

Why is RNA so unstable compared to DNA?

A

RNA doesn’t have protection signals which means the get attacked by RNA cleaving enzymes

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53
Q

What is the base difference in RNA when compared to DNA?

A

Thymine (DNA) to Uracil (RNA)

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54
Q

What is the sugar difference in RNA when compared to DNA?

A

deoxyribose (DNA) to ribose (RNA)

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55
Q

What is transcription?

A

The conversion / copy of DNA to RNA

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56
Q

What direction does transcription run with respect to the coding strand?

A

5’ to 3’

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57
Q

What are the base pairs in DNA?

A

A with T (2 hydrogen bonds)
C with G (3 hydrogen bonds)

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58
Q

What is the diameter of DNA?

A

2 nm

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59
Q

What microtubule does not disassemble very often?

A

Intermediate filaments

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60
Q

What microtubule is not present in plants or fungi?

A

Intermediate filaments

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61
Q

What is the diameter of intermediate filaments?

A

~10 nm

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62
Q

What is the diameter of microtubules?

A

24 nm

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63
Q

What is the diameter of actin filaments?

A

8 nm

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64
Q

What is the transport motor for actin?

A

Myosin

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65
Q

What is the outwards charge in microtubules ?

A

Positive

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66
Q

Where are new tubulin hetero-dimers added to microtubules?

A

The positive end

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67
Q

What is the motor that walks to the minus end of tubules?

(inwards)

A

dynein motor

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68
Q

What motor walks to the plus end of tubules?

(outwards)

A

Kinesin

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69
Q

What is in the center of mammalian centrosomes?

A

A pair of centrioles

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70
Q

What changes/defines cellular structure?

A

Actin filaments

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71
Q

What are the actin modifying proteins?

(there are 9)

A

Nucleating Protein
Monomer-Sequestering Protein
Severing Protein
Cross-Linking Protein
Capping (plus-end blocking) Protein
Side-Binding Protein
Myosin Motor Protein
Bundling Protein
Branching Protein

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72
Q

How many types of actin are there in the human genome?

A

six

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73
Q

What is the most abundant intracellulara protein?

A

Actin

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74
Q

What are the three cytoskeleton filaments?

A

Actin Filaments
Intramediate Filaments
Microtubules

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75
Q

What ions do muscle cells intake?

A

Calcium ions

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76
Q

What channels are at the synapse?

A

Calcium channels

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77
Q

What does the innactivation phase of neurons prevent?

A

The action potential from running in two directions

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78
Q

What ion rushes into neurons?

A

Na+ (sodium)

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79
Q

What neuron state is not sensative to membrane potentials?

A

The inactivated state

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80
Q

Name the types of passive transport?

A

simple diffusion
channel mediated
transporter mediated

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81
Q

What is the electrochemical gradient?

A

It is the concentration gradient and membrane potential together

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82
Q

What does the electrochemical gradient determine?

A

It predicts ion flux

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83
Q

What transports soluable molecules across membranes?

A

Transporter proteins

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84
Q

What must you know to understand ion flux?

A

Concentration gradient and membrane potential

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85
Q

What is osmolarity?

A

The concentration of soluable particles

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86
Q

What allows ion transfer across membranes and exhibits speciificty?

A

Channels

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87
Q

Do channels or tranport proteins have the ability to move against the gradient?

A

Transport proteins

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88
Q

What are the three types of lipid movement?

A

lateral diffusion, flexion, and rotation

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89
Q

what does a more structured lipid membrane mean for the membrane?

A

A less fluid membrane

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90
Q

What does temperature do to a lipid membrane?

A

increases fluidity

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91
Q

what do unsaturated fatty acids do to a lipid membrane?

A

increase fluidity

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92
Q

What does cholesterol do to a lipid membrane?

A

decreases fluidiity by filling in gaps

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93
Q

Are gel-like or fluid-like membranes thicker?

A

Gel-like

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94
Q

What does FRAP stand for?

A

Fluorescence Recovery After Photobleaching

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95
Q

What does FRAP indicate?

A

Lipid membrane dynamics.

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96
Q

What does a faster FRAP mean?

A

faster lipid movement

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97
Q

True or False?

Lipid composition of membranes is the same in all organelles.

A

False

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98
Q

True or False?

The lipid compositon of membranes is adjusted to temperature.

A

True

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99
Q

True or False?

Lipid membrane composition is adjusted to function.

A

True

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100
Q

True or False?

Lipid membrane composition is the same on each side of the bi-layer.

A

False

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101
Q

What are the four membrane associated protein types?

A

Transmembrane
Monolayer-associated a helix
lipid linked
protein attached

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102
Q

Which of the four membrane associated protein types is salt extractable?

A

Protein-attached

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103
Q

What do detergents have?

A

A high CMC

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104
Q

What do detergents do?

A

Solubilize transmembrane proteins and membranes

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105
Q

What is the most common structure for the transmembrane domain of proteins?

A

a-helix

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106
Q

What do the hydrophobic side chains of transmembrane protein AA face?

A

the lipids

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107
Q

Aproximately how long are the transmembrane domains of transmembrane proteins?

A

~20-25 hydrophobic amino acids

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108
Q

What is a hydrophobicity profile?

A

The description of how hydrophobic an amino acid is

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109
Q

What does a posative hydrophobicity indicate?
What does a negative hydrophobicity indicate?

A

Posative - hydrophobic
negative - hydrophilic

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110
Q

What are the functions of transmembrane proteins?

A

nutrient and ion import/export
structural support
cell signaling/sensing
enzymatic work

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111
Q

True or False?

Water can permeate membranes.

A

True, but not very fast

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112
Q

What can easily get through membranes?

A

small, uncharged molecules

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113
Q

What cannot get through membranes?

A

Ions

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114
Q

What influences membrane permeability?

A

lipid composition, fluidity, and consistency

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115
Q

What do aquaporins do?

A

allow for the fast exchange of water but not ions

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116
Q

What is osmolarity?

A

the total concentration of all solute particles

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117
Q

What is trugor pressure.

A

the pressure created by water being drawn into the cell

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118
Q

What does turgor pressure do?

A

It helps maintatin cell structure

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118
Q

What is a concentration gradient?

A

A higher concentration of molecules on one side of a membrane compared to the other

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119
Q

What is membrane potential?

A

Unequal charge distribution across the membrane

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120
Q

What do we call the concentration gradient and membrane potential when looked at together?

A

the electrochemical gradient

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121
Q

What does the electrochemical gradient determine?

A

Which way charged solutes move across a membrane

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122
Q

What do transporter proteins contain?

A

a central binding site

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123
Q

What happens when a molecule binds the binding site of a transporter protein?

A

The protein changes which side is accessable.

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124
Q

What do transporter proteins transport?

A

molecules and nutrients

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125
Q

True or False?

Channels are just pores.

A

False
they are pores but they are also selective

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126
Q

Why is glucose considered active transport if movement across the membrane requires no energy?

A

energy is used to trap the glucose

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127
Q

True or False?

Transport across membranes can be coupled to ion gradients?

A

True

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128
Q

What gradient is used for nutrient transport in plants and fungi?

A

proton gradient

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129
Q

What gradient is used for nutrient transport in animal cells?

A

sodium gradient

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130
Q

How many essential amino acids are there?

A

8

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131
Q

What are the two ways cells get new amino acids?

A

through import or synthesis from glucose

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132
Q

Do ion channels allow for water to flow through them?

A

No

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133
Q

What are the four gating mechanisms of channels?

A

voltage-gating
ligand-gated (extracellular)
ligand-gated (intracellular)
mechanically-gated

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134
Q

Describe the TRPV1 channel

A

found in the plasma membrane of neurons, it functions as a pain receptor allowing ions to flux when activated by heat or capsaicin

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135
Q

Are dendrites or axons the long arms on neurons?

A

axons

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136
Q

Where do neurons recieve information from other neurons?

A

dendrites

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137
Q

What is action potential?

A

the rapid and local change of membrane potential propagating along the membrane of neurons

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138
Q

What ion fluxes into the cell causing a membrane potential shift in neurons?

A

sodium ions

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139
Q

What does a negative membrane potential indicate?

A

the cytosolic side of the membrane is negative

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140
Q

What is the membrane potential of a resting neuron?

A

~50mV

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141
Q

What is the membrane potential of an activated neuron?

A

~40mV

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142
Q

What does the inactivation state of neuron channels ensure?

A

Action potential directionality

143
Q

What are the lengths of axons?

A

less than 1mm to more than 1m

144
Q

What is the space between the presynaptic nerve terminal and postsynaptic membrane called?

A

synaptic cleft

145
Q

What happens when the action potential reaches the end of a neuron?

A

calcium channels get opened

146
Q

What are neurotransmitters?

A

small chemicals used for cell signaling

147
Q

What does the presenese of calcium do at the end of an axon?

A

causes the fusion of synaptic vesicles resulting in the release of neurotransmitters

148
Q

What happens after neurotransmitters are released?

A

neurotransmitters diffuse across the synaptic cleft binding to an opening a cation channel

149
Q

What are the three filament types?

A

actin, microtubules, and intermediate filamnets

150
Q

Describe actin structure.

A

twisted two strand 8-9 nm diameter

151
Q

Describe MT structure.

A

hollow tube, 24 nm

152
Q

Describe IF structure.

A

rope like, 10nm diameter

153
Q

Where does actin localize?

A

the edges of the cell

154
Q

What is the most abundant intracellular protein?

A

actin

155
Q

How many forms of actin are encoded in the human genome?

A

six

156
Q

What end of actin is the ATP binding site accessible?

A

the minus end

157
Q

What is g actin?

A

the globular monomer form of actin

158
Q

What is f actin?

A

actin polymer with structural and functional polarity

159
Q

What end of F actin is new G actin added?

A

the plus end

160
Q

What happens to the ATP on G actin when it binds to F actin?

A

a phosphate group is lost and it turns into adp

161
Q

what is the actin motor?

A

myosin

161
Q

What does actin sequestering protein do?

A

keeps actin monomers from polymerizing

162
Q

What do the proteins fimbrin and filamin do?

A

cross link actin

163
Q

How are the proteins fimbrin and filamin different?

A

fimbrin is small and bundles actin while filamin is long, flexiable, and forms actin networks

164
Q

What is the cell cortex?

A

the periphiry region of the cell where actin forms a dense network

165
Q

True or False?

The cortex is not dynamic.

A

False

166
Q

What do actin networks do?

A

Shape, move, and divide cells

167
Q

What does the activation of platelets do to the actin network?

A

actin reorginizes and flattens out the cell

168
Q

What end does actin polymerize at?

A

the plus end

169
Q

What filament is asociated with myosin motors?

A

actin

170
Q

What end of actin is oriented towards the plasma membrane?

think about how actin growth and cell growth relate

A

The posative end

171
Q

What is the Arp2/3 (ARP) complex?

A

A protein that forms new actin branches

172
Q

What end does actin dissasemble at?

A

the minus end

173
Q

What are the domains of myosin motors?

A

The head, neck, and tail domains

174
Q

What end of myosin binds to the substrate?

A

tail end

175
Q

What binds to the head domain of myosin and generates force?

A

ATPases

176
Q

What direction do myosin motors walk?

A

towards the posative end of actin

177
Q

How much force can an actin motor generate?

A

3-5pN

178
Q

How do muscles contract?

A

myosin motors pull two regions of actin filament together

179
Q

Where do centrosomes localize?

A

the perinuclear region

180
Q

what is a tubulin subunit made of

A

one alpha + one beta tubulin

181
Q

In microtubules what tubulin is bound to GTP and which is bound to GDP?

A

alpha-GTP
beta-GDP

182
Q

which tubulin hydrolizes the nucleotide?

A

Beta

183
Q

Which tubulin represents the plus end of microtubules?

A

Beta

184
Q

What are microtubules made of?

A

protophilaments

185
Q

what are protophilaments made of?

A

tubulin dimers

186
Q

what do protophilaments look like?

A

lines of tubulin subunits bound minus end to plus end

187
Q

True or False?

Microtubules are much more rigid than actin.

A

True

188
Q

What stabilizes MT ends?

A

GTP cap

189
Q

What happens if GTP tublin adds slower to MT than GTP hydrolysis?

A

MT dissasembles

190
Q

What end are new tubulin dimers added to the MT?

A

The plus end

191
Q

what do gamma tubulin ring complex do?

A

nucleate MT growth

192
Q

What is found inside the centrosome?

A

A pair of centrioles

193
Q

True or False?

Centrioles are found in all eukaryotes?

A

False

194
Q

describe the structure of centrioles?

A

protohilament triplets aranged into a cylinder

195
Q

What are the MT motors?

A

Dynein and Kinesin

196
Q

What direction does kinesin walk?

A

The plus end

197
Q

What direction does dynein walk?

A

The minus end

198
Q

True or False?

Microtubules help distibute and localize organelles.

A

False.

The MT and motors are what do this function

199
Q

True or False?

The primary cilia is found in almost all mammalian cells.

A

True

200
Q

What does the primary cilia do?

A

mechanical sensing and signaling

201
Q

What is a basal body?

A

the nucleating strucutre for MT at the bottom of a cilia
They are centrioles

202
Q

What causes the flagellum of sperm to move?

A

dynein motors move MT against each other

203
Q

What is the flagellum of sperm cells filled with?

A

Mitochondria

204
Q

True or False?

Kinesin and Myosin work together for cellular transport at the cell cortex.

A

True

205
Q

True or False?

IF are found in all eukaryotes.

A

False
they are only found in animal cells

206
Q

What is the main role of IF?

A

Structural support

207
Q

Describe the structure of IF.

A

a-helix monomers dimerize and coil around each other
two dimers form a tetramer
8 tetramers form a IF subunit which add together to form IF

208
Q

Where are IF found?

A

all throughout the cytoplasm

209
Q

What is the nuclear lamina?

A

Essentially the same as the cell cortex but inside the nucleus and made of IF instead of actin

210
Q

What carbon is the base of a nucleotide bound to?

A

the 1’ carbon

211
Q

What carbon is the phosphate bound to on a nucleotide?

A

the 5’ carbon

212
Q

What is the central dogma of molecular biology?

A

DNA encodes information which is tranfered into RNA which is tranfered into proteins

213
Q

What is gene expression?

A

How the information stored in dna is used to produce protein

214
Q

What is a codon?

A

three base pairs in sequence

215
Q

How many codons code for the stop codon?

A

three

216
Q

What is the start codon sequence?

A

ATG

217
Q

What base changes to what in RNA

A

T in DNA changes to U in RNA

218
Q

True or False?

The size of the genome correlates with the number of chromesomes.

A

False

219
Q

True or False?

The sum of nuclear DNA is reffered to as the genome?

A

True

220
Q

What is eukaryotic DNA packaged into?

A

chromesomes

221
Q

How many chromesomes are in the human genome?

A

2 x 23

222
Q

When are chromesomes the most compact? When are they the least compact?

A

Most compact - mitosis
least compact - interphase

223
Q

What is heterochromatin, where is it, and what does it look like.

A

dense regions of chromesome, the nucleus, dark spots

224
Q

True or False?

The outer nuclear membrane is distinct from the ER?

A

False
they are continuous with one another

225
Q

What is the space inbetween nuclear membranes called?

A

the perinuclear space

226
Q

What size particles can diffuse through nuclear pores?

A

<60kDa or 9nm

227
Q

What is the largest particle that can travel through nuclear pores?

A

26nm

228
Q

What structure sperates the outer and inner nuclear membrane?

A

nuclear pores

228
Q

What does transcription do?

A

Makes an RNA copy of one strand of DNA

229
Q

What is RNA a copy of?

A

the coding strand of DNA

230
Q

Where is the alcohol group on RNA?

A

the 2’ carbon

231
Q

What protein transcribes DNA into RNA?

A

RNA ploymerase

232
Q

What is the thing on tRNA which mathces up with the mRNA codon called?

A

anticodon

233
Q

True or False?

RNA can have enzymatic functionality.

A

True

234
Q

What, upstream of a gene, initiates transcription?

A

Promoter sequence

235
Q

What is contained in the promoter sequence?

A

the TATA box

236
Q

What does the TATA box do?

A

recruits general transcription factors

237
Q

what do general transcription factors do?

A

recruit RNA polymerase 2
seperate DNA strands

238
Q

**

What direction does transcription run?

A

5’ to 3’ of the coding strand

239
Q

What happens to RNA polymerase before it starts making new RNA?

A

the RNA tail is phosphorylated

240
Q

What is the speed of of Transcription?

A

20-70 bases per second

241
Q

What is done as soon as the 5’ end of mRNA is accessible?

A

A 5’ cap is added to the 5’ end of mRNA

242
Q

What is the poly A tail and where is it found?

A

a long(100-250 base) chain of adenine added to the 3’ end of mRNA

243
Q

what are the steps of pre-mRNA processing?

A

5’ capping
polyA site cleavage
addition of the polyA tail
RNA splicing (removing introns)

244
Q

what are introns?

A

non coding regions of a gene that are removed in mRNA processing

245
Q

what is splicing?

A

the removal of introns from mRNA

246
Q

what does mRNA splicing?

A

spliceosome

247
Q

What is alternative splicing and how common is it?

A

different mRNA molecules resulting from the same gene and it is very common (95% of human genome does this)

248
Q

When does mRNA leave the nucleus?

A

once it has fully matured

249
Q

What is translation?

A

the decoding of mRNA and production of the coresponding protein

250
Q

What does translation require?

A

mRNA, ribosomes, and tRNA

251
Q

True or False?

Ribosomes are among the largest and most abundant protein complexes in cells.

A

True

252
Q

What are the subunits of ribosomes?

A

the large and small subunits

253
Q

what is the size of the small ribosomal subunit?

A

40 S

254
Q

What is the size of the large ribosomal subunit?

A

60 S

255
Q

What is the size of the complete ribosomal structure?

A

80 S

256
Q

True or False?

RNA is a structural component of ribosomes.

A

True

257
Q

What are the three binding sites of ribosomes?

A

E site, P site, and A site

258
Q

How can the 30-40 tRNA types cover for all 64 possible codons?

A

The thrid position in the anticodon can “wobble” or mis-align to form a match

259
Q

What does tRNA synthetase do?

A

links the proper amino acid to the proper tRNA

260
Q

What AA is encoded by ATG(the start codon)

A

Methionine

261
Q

What direction does translation happen?

A

5’ to 3’ of the mRNA

262
Q

What is the first step of translation?

A

the small ribosomal subunit with an initiator tRNA scan the mRNA for a start codon

263
Q

What is the second step of translation?

A

initiation factors leave the small ribosomal subunit once a start codon is found and the large ribosomal subunit binds

264
Q

What is the third step of translation?

A

new tRNA binds the A site of the ribosome and a peptide bond is formed between the two AA

265
Q

What direction are new proteins synthesized?

A

N terminus to C terminus

266
Q

What is the fifth step of translation?

A

the large subunit moves forward shifting the tRNAs from the P and A sites to the E and P sites respectively

267
Q

What is the sixth step of translation?

A

the small subunit shifts forward ejecting the used tRNA from the E site

268
Q

What terminates translation?

A

A release factor binds the stop codon causing hydrolysis and the release of the polypeptide form the last tRNA

269
Q

What is the mRNA and ribosome complex called?

A

a polysome

270
Q

True or False?

The protein waits to fold until its polypeptide is completly synthesized?

A

False

271
Q

True or False?

Protein folding typically happens in sections which are the protein domains.

A

True

272
Q

Do chaperones require energy?

A

Yes and they use ATP

273
Q

True or False?

Many proteins require chaperones.

A

True

274
Q

What are the functions of the ER?

A

protein translocation
protein folding
protein glycosylation
protein Quality control
calcium ion storage

275
Q

what proteins are synthesized at the ER?

A

transmembrane and translumen proteins

276
Q

What binds to ribosomes to ensure proper polypeptide insertion into the ER or lumen?

A

protein translocators

277
Q

What does SRP stand for and what does it do?

A

Signal recognition particle
it binds the N terminus of a new polypeptide and directs it to the SRP receptor at the ER

278
Q

Once the SRP has bound what happens next?

A

The ribosome binds a translocator and continues polypeptide synthesis

279
Q

When is the translocator open?

A

only when ribosomes are bound to them

280
Q

Once translocation into the ER lumen has begun what happens?

in soluable lumen proteins

A

the signal sequence is cleaved off

281
Q

What happens when a transmembrane domain reaches a translocator?

A

the transmembrane domain is ejected into the ER membrane , the ribosome detatches from the translocator, and polypeptide synthesis continues into the cytoplasm

282
Q

How do protteins with two or more transmembrane domains get synthesized?

A

A start transfer sequence tells the ribosome to bind the translocator and synthesize into the lumen
a stop stransfer sequence does the opposite

283
Q

What is protein glycosylation?

A

the adition of polysacharides (sugar chains) to AA

284
Q

Why is glycosylation useful?

A

It helps the cell recognize foreign vs invader proteins
it also icreases the stability of proteins

285
Q

True or False?

Only a few proteins at the ER get glycosylated?

A

False
most proteins are glycosylated

286
Q

What proteins are allowed to leave the ER?

A

folded proteins only

287
Q

Where do newly translated proteins fold?

A

The ER

288
Q

What happens if proteins do not fold correctly?

A

They are kicked out of the ER (using translocators), ubiquinated, and degraded in proteasomes

289
Q

how do folded ER poteins get to the golgi?

A

ER budded transport vesicles

290
Q

How are soluable proteins sorted into vesicles?

A

by binding receptors

291
Q

How are transmembrane proteins sorted into vesicles?

A

by binding coat proteins

292
Q

After a ER vesicle is formed what happens to it?

A

it uncoats, tethers the golgi, docks, and fuses with the golgi membrane

293
Q

What are RAB proteins?

A

Small GTPases that act as regulators/switches

294
Q

What determines if a GTPase is on or off?

A

if it has a bound GTP (on) or a bound GDP (off)

295
Q

What is the final barrier in vesicle fusion to a membrane and how is it overcome?

A

The final barrier is a thin film of water
snares break through this barrier

296
Q

How do snares work?

A

v snares on the viscle dimerize and twist around t snares on the target membrane thus drawing the vesicle closer to the membrane

297
Q

What is the main function of the golgi?

A

protein sorting

298
Q

which side of the golgi recieves vesicles and what side sends them away?

A

cis recieves and trans transports away

299
Q

what are the two secretory pathways?

A

constitutive secretion and regulated secretion

300
Q

which secratory pathway do plasma membrane proteins use?

A

constitutive secretion

301
Q

Describe how insulin gets released?

A

Glucose yeilds high ATP which closes potassium channels.
This depolarizes the membrane thus opening calcium channels.
Calcium presense signals the binding of vesicles and release of insulin outside the cell

302
Q

Where do lots of cell signaling and transport functions localize?

A

the cell surface

303
Q

What are eisosomes?

A

Wrinkles in the cell membrane which store membrane proteins

304
Q

What is phagocytosis and what cells do it?

A

the engulfing of large particels (a form of endocytosis)
performed by macrophages

305
Q

How is phagocytosis done?

A

the membrane wraps around the object being endocytosed

306
Q

What is pinocytosis?

A

the uptake of fluid filled vesicles
~100nm diameter

307
Q

What are the two types of clathrin and what do they do?

A

Heavy and Light chain
they assemble into a cage which deformes the membrane

308
Q

What do adaptors do?

A

they link cargo recptors or transmembrane proteins and clathrin proteins

309
Q

What makes LDL interesting?

A

it has a monolayer membrane

310
Q

What does LDL transport?

A

cholesterol and fat

311
Q

What do early endosomes do?

A

recieve endocytic vesicles and recycle a portion of the material back to the cell membrane

312
Q

What is the other name for late endosomes?

A

Multi Vesicular Bodies (MVB)

313
Q

What do late endosomes do?

A

they package membrane and proteins into the lumen and deliver their contents to lysosomes for degredation

314
Q

What is the function of lysosomes?

A

degrade macromolecule and store AA and salts

315
Q

Describe the inside of Lysosomes.

A

Acidic and full of hydrolytic enzymes

316
Q

what does protein degredation?

A

proteases

317
Q

where are transmembrane proteins degraded?

A

the lysosome

318
Q

where are cytoplasmic proteins degraded?

A

the proteosomes

319
Q

What is the function of Ubiquitin (UB)?

A

tag things for degredation

320
Q

what end of UB binds to the target protein?

A

the c terminus

321
Q

True or False?

Only one UB binds to a protein to mark it for degredation.

A

False
A chain of UB binds to the protein

322
Q

what does the E1 protein do?

A

binds free floating UB and prepes it

323
Q

What does the E2 protein do?

A

Takes UB from E1 and attaches itself to E3

324
Q

What does the E3 protein do?

A

Links the target protein with UB

325
Q

describe the structure of proteasomes.

A

A core tube with identical caps on either end

326
Q

What is used for energy to put UB tagged proteins into proteasomes?

A

ATP

327
Q

How does the proteasome work?

A

the cap unfolds the protein and feed the polypeptide into the core
the core cleaces the protein into small peptides
the opposite cap ejects the degraded material

328
Q

describe the late endosomal pathway.

A

a cell surface protein gets ubiquinated and endocytosed in a clathrin coated vesicle
at the late endosome the UB tagged proteins get injested with the help of ESCRTS forming internal vesicles
the late endosome delivers these vesicles to the lysosome
the lysosome degrades its contents

329
Q

what side are ESCRT proteins found on a membrane

A

cytoplasmic
on the cell membrane, vesicles, and endosomes

330
Q

True or False?

ESCRT proteins play a sorting role on late endosomes.

A

True

331
Q

Describe the ESCRT mechanism.

A

No, it is not yet understood how ESCRTs deform away from themselves

332
Q

Where are late endosomal vesicles and their contents degraded?

A

the lysosome

333
Q

what is autophagy?

A

the degredation of large cellular structures and particles

334
Q

True or False?

Autophagy is the general term for all organelle degredation.

A

True, but each organelles degredation has its own name

335
Q

What induces autophagy?

A

starvation

336
Q

Describe the structure of autophagosomes.

A

double membrane vesicls

337
Q

How do autophagosomes work?

A

they encompas their contents and then bind to the lysosomes

338
Q

what is mitophagy?

A

the degredation (autophagy) of mitochondria

339
Q

True or False?

The monmers and degraded material form lysosomes can be reused?

A

True

340
Q

What types of cells will continuously divid?

A

Stem cells

341
Q

What are the phases of the cell cycle?

A

G0, G1, S, G2, and M

342
Q

What happens in the G0 phase?

A

Differentiation occurs where cells decide if they are stem and will replicate or if they are functional

343
Q

Generally speaking what controls the cell cycle?

A

CDKs

344
Q

What do CDKs do?

A

phosphorylate (thus regulate) initiation and regulation proteins

345
Q

What is phosphorylation?

A

the addition of a phospahte group to something
things are often inactive without a phospahte group on them thus phosphorylation is an activating reaction.

346
Q

how does cyclin regulate the cell cycle?

A

Cyclin binds to CDKs activing them
Activated CDKs phosphorylate and thus activate initator/regulatory proteins
those proteins activate phases of the cell cycle

347
Q

What does degredation of cyclin do?

A

ensures directionality of the cell cycle and signals the end of a phase

348
Q

What does the p27 protein do?

A

inhibits cyclin activated CDKs

349
Q

How do activated CDKs get inhibited by a kinase?

A

the kinase adds an inhibtory phosphaate group which is later removed by an activating phosphotase (cdc25)

350
Q

What are the different ESCRT proteins?

A

ESCRT-0, ESCRT-I, ESCRT-II, ESCRT-III, Vps4

351
Q

What is the protein that sreves a checkpoint funtion at spindle assembly?

A

APC

352
Q

What protein binds to the kineticor until MT bind and take their place?

A

Mad2 proteins

353
Q

What does the release of Mad2 Protein do?

A

allows for the release of cdc20

354
Q

What does released cdc20 bind to?

A

APC

355
Q

what binds sister chromatids together and gets cut to start anaphase?

A

cohesin rings

BIOL 2020 (4 decks)

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